Job ID = 6498645 SRX = SRX647443 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T00:17:42 prefetch.2.10.7: 1) Downloading 'SRR1508426'... 2020-06-26T00:17:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:19:37 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:19:37 prefetch.2.10.7: 1) 'SRR1508426' was downloaded successfully Read 16994852 spots for SRR1508426/SRR1508426.sra Written 16994852 spots for SRR1508426/SRR1508426.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:31 16994852 reads; of these: 16994852 (100.00%) were unpaired; of these: 5507390 (32.41%) aligned 0 times 8768169 (51.59%) aligned exactly 1 time 2719293 (16.00%) aligned >1 times 67.59% overall alignment rate Time searching: 00:09:31 Overall time: 00:09:31 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2276348 / 11487462 = 0.1982 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 09:36:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX647443/SRX647443.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX647443/SRX647443.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX647443/SRX647443.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX647443/SRX647443.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 26 Jun 2020 09:36:03: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:36:03: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:36:13: 1000000 INFO @ Fri, 26 Jun 2020 09:36:22: 2000000 INFO @ Fri, 26 Jun 2020 09:36:31: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 09:36:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX647443/SRX647443.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX647443/SRX647443.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX647443/SRX647443.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX647443/SRX647443.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 26 Jun 2020 09:36:33: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:36:33: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:36:40: 4000000 INFO @ Fri, 26 Jun 2020 09:36:43: 1000000 INFO @ Fri, 26 Jun 2020 09:36:49: 5000000 INFO @ Fri, 26 Jun 2020 09:36:52: 2000000 INFO @ Fri, 26 Jun 2020 09:36:58: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 09:37:01: 3000000 INFO @ Fri, 26 Jun 2020 09:37:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX647443/SRX647443.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX647443/SRX647443.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX647443/SRX647443.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX647443/SRX647443.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 26 Jun 2020 09:37:03: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:37:03: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:37:07: 7000000 INFO @ Fri, 26 Jun 2020 09:37:10: 4000000 INFO @ Fri, 26 Jun 2020 09:37:13: 1000000 INFO @ Fri, 26 Jun 2020 09:37:17: 8000000 INFO @ Fri, 26 Jun 2020 09:37:19: 5000000 INFO @ Fri, 26 Jun 2020 09:37:22: 2000000 INFO @ Fri, 26 Jun 2020 09:37:26: 9000000 INFO @ Fri, 26 Jun 2020 09:37:28: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 09:37:28: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 09:37:28: #1 total tags in treatment: 9211114 INFO @ Fri, 26 Jun 2020 09:37:28: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:37:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:37:28: #1 tags after filtering in treatment: 9211114 INFO @ Fri, 26 Jun 2020 09:37:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:37:28: #1 finished! INFO @ Fri, 26 Jun 2020 09:37:28: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:37:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:37:29: #2 number of paired peaks: 137 WARNING @ Fri, 26 Jun 2020 09:37:29: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Fri, 26 Jun 2020 09:37:29: start model_add_line... INFO @ Fri, 26 Jun 2020 09:37:29: 6000000 INFO @ Fri, 26 Jun 2020 09:37:29: start X-correlation... INFO @ Fri, 26 Jun 2020 09:37:29: end of X-cor INFO @ Fri, 26 Jun 2020 09:37:29: #2 finished! INFO @ Fri, 26 Jun 2020 09:37:29: #2 predicted fragment length is 101 bps INFO @ Fri, 26 Jun 2020 09:37:29: #2 alternative fragment length(s) may be 101,571 bps INFO @ Fri, 26 Jun 2020 09:37:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX647443/SRX647443.05_model.r WARNING @ Fri, 26 Jun 2020 09:37:29: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:37:29: #2 You may need to consider one of the other alternative d(s): 101,571 WARNING @ Fri, 26 Jun 2020 09:37:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:37:29: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:37:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:37:31: 3000000 INFO @ Fri, 26 Jun 2020 09:37:38: 7000000 INFO @ Fri, 26 Jun 2020 09:37:41: 4000000 INFO @ Fri, 26 Jun 2020 09:37:47: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:37:47: 8000000 INFO @ Fri, 26 Jun 2020 09:37:50: 5000000 INFO @ Fri, 26 Jun 2020 09:37:56: 9000000 INFO @ Fri, 26 Jun 2020 09:37:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX647443/SRX647443.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:37:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX647443/SRX647443.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:37:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX647443/SRX647443.05_summits.bed INFO @ Fri, 26 Jun 2020 09:37:57: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1583 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:37:58: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 09:37:58: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 09:37:58: #1 total tags in treatment: 9211114 INFO @ Fri, 26 Jun 2020 09:37:58: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:37:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:37:58: #1 tags after filtering in treatment: 9211114 INFO @ Fri, 26 Jun 2020 09:37:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:37:58: #1 finished! INFO @ Fri, 26 Jun 2020 09:37:58: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:37:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:37:58: #2 number of paired peaks: 137 WARNING @ Fri, 26 Jun 2020 09:37:58: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Fri, 26 Jun 2020 09:37:58: start model_add_line... INFO @ Fri, 26 Jun 2020 09:37:59: start X-correlation... INFO @ Fri, 26 Jun 2020 09:37:59: end of X-cor INFO @ Fri, 26 Jun 2020 09:37:59: #2 finished! INFO @ Fri, 26 Jun 2020 09:37:59: #2 predicted fragment length is 101 bps INFO @ Fri, 26 Jun 2020 09:37:59: #2 alternative fragment length(s) may be 101,571 bps INFO @ Fri, 26 Jun 2020 09:37:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX647443/SRX647443.10_model.r WARNING @ Fri, 26 Jun 2020 09:37:59: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:37:59: #2 You may need to consider one of the other alternative d(s): 101,571 WARNING @ Fri, 26 Jun 2020 09:37:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:37:59: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:37:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:37:59: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:38:08: 7000000 INFO @ Fri, 26 Jun 2020 09:38:16: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:38:17: 8000000 INFO @ Fri, 26 Jun 2020 09:38:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX647443/SRX647443.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:38:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX647443/SRX647443.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:38:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX647443/SRX647443.10_summits.bed INFO @ Fri, 26 Jun 2020 09:38:26: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (906 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:38:26: 9000000 INFO @ Fri, 26 Jun 2020 09:38:28: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 09:38:28: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 09:38:28: #1 total tags in treatment: 9211114 INFO @ Fri, 26 Jun 2020 09:38:28: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:38:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:38:28: #1 tags after filtering in treatment: 9211114 INFO @ Fri, 26 Jun 2020 09:38:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:38:28: #1 finished! INFO @ Fri, 26 Jun 2020 09:38:28: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:38:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:38:29: #2 number of paired peaks: 137 WARNING @ Fri, 26 Jun 2020 09:38:29: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Fri, 26 Jun 2020 09:38:29: start model_add_line... INFO @ Fri, 26 Jun 2020 09:38:29: start X-correlation... INFO @ Fri, 26 Jun 2020 09:38:29: end of X-cor INFO @ Fri, 26 Jun 2020 09:38:29: #2 finished! INFO @ Fri, 26 Jun 2020 09:38:29: #2 predicted fragment length is 101 bps INFO @ Fri, 26 Jun 2020 09:38:29: #2 alternative fragment length(s) may be 101,571 bps INFO @ Fri, 26 Jun 2020 09:38:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX647443/SRX647443.20_model.r WARNING @ Fri, 26 Jun 2020 09:38:29: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:38:29: #2 You may need to consider one of the other alternative d(s): 101,571 WARNING @ Fri, 26 Jun 2020 09:38:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:38:29: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:38:29: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:38:46: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:38:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX647443/SRX647443.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:38:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX647443/SRX647443.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:38:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX647443/SRX647443.20_summits.bed INFO @ Fri, 26 Jun 2020 09:38:56: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (500 records, 4 fields): 1 millis CompletedMACS2peakCalling